Question: How to extract sequences from multiple fasta files according to my list files
0
gravatar for sohjiro4321
3.4 years ago by
Taipei, R.O.C
sohjiro43210 wrote:

I have done orthologous analysis in four fasta files from four different species. After orthologous analysis, I obtain orthologous gene list. For example: orthologous gene 1: 1st species (gene_id1), 2nd species (gene_id2), 3rd species (gene_id3), 4th species (gene_id4) orthologous gene 2: 1st species (gene_id1'), 2nd species (gene_id2'), 3rd species (gene_id3'), 4th species (gene_id4') ......

I would like to extract sequences from each fasta files from different species and put them into separate fasta files according to list. How could I perform these requests?

blast sequence • 927 views
ADD COMMENTlink modified 3.4 years ago by EVR570 • written 3.4 years ago by sohjiro43210
1
gravatar for EVR
3.4 years ago by
EVR570
Earth
EVR570 wrote:

seqtk subseq -l 100000 input.fasta gene_list.txt

ADD COMMENTlink written 3.4 years ago by EVR570

thank you for providing information. May I ask a further question? Would there be specific format in gene_list.txt? And by the way, I have four input.fasta. How do I extract orthologous sequences from four independent fasta into each orthologous gene fasta files?

ADD REPLYlink written 3.4 years ago by sohjiro43210
1
gene_list.txt

gene_id1 gene_id2 gene_id3

Use the above command separately for every fasta file you have

ADD REPLYlink written 3.4 years ago by EVR570
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